Consistent structured output: `--json` on all commands + Markdown default

[patrikbraborec]

Summary

CLI output needs to be consistently structured for both human and programmatic consumption.

Action Items

• --json must work on all commands (39 commands currently lack it) — except --help (we do not need to support JSON for --help)
• Default output should use Markdown + colors (inspired by mcpc — good for both humans and LLMs)

Notes

• Tables are great for humans, less critical for agents

Supersedes

• Add in a flag to make commands output machine-readable results instead of human readable ones #566 (Add in a flag to make commands output machine-readable results instead of human readable ones)
• Add --markdown output flag for CLI commands #1050 (Add --markdown output flag for CLI commands)